LZ4Net is just LZ4 compression/decompression. It doesn't deal with zip-files which are fully structured and path designated, example: a zip file may contain numerous "files" under a path designation (it's still a flat tree). LZ4 while usable for zip file compression just operates on a blob of data, there will be no structure that you did not create yourself before compressing.

Unity's asset bundles are their own file format, so they can use any compression they want. We use LZ4 inside the XNB file when content compression is selected. What you want is a container format that allows many files to be inside a container file. Zip can be used for that, or you can provide your own container format. I have done both successfully in the past.